Dear Amber Users
I was able to find the partial molar volume of a real protein through
rism3d.snglpnt in AMBER.
Can anyone suggest how we can find the partial molar volume of hypothetical
protein molecule without atomic charges?? I mean how to switch off the
electrostatic interaction term?
What I have tried is explained below:
The long range electrostatic term or the real asymptotic part of the total
and direct correlation function is calculated separately in 3D-RISM theory
using '-asymp' root, I have tried to calculate the total correlation
function of hypothetical molecule by subtracting the product of charge on
solvent atom and asymptotic part from rism calculations on AMBER from the
total correlation function of real molecule.
But I am getting higher total correlation function of hypothetical molecule
in comparison to that of real molecule. Due to negative charge of solvent
oxygen atom the asymptotic term of the total correlation function gets
added up to total correlation function of the real molecule which leads to
the higher values of the total correlation function of hypothetical
molecule without atomic charges.
Is the method correct??
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Received on Sat Jul 21 2018 - 03:00:02 PDT
